HEADER IMMUNE SYSTEM 26-APR-13 4BKL TITLE CRYSTAL STRUCTURE OF THE ARTHRITOGENIC ANTIBODY M2139 (FAB FRAGMENT) TITLE 2 IN COMPLEX WITH THE TRIPLE-HELICAL J1 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: M2139 FAB FRAGMENT HEAVY CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: VH AND CH1; COMPND 5 OTHER_DETAILS: HEAVY CHAIN CLEAVED BY PAPAIN, EXACT TERMINI UNCLEAR; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: M2139 FAB FRAGMENT LIGHT CHAIN; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: VL AND CL; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: J1 EPITOPE; COMPND 12 CHAIN: E, F, G; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: TRIPLE-HELICAL SYNTHETIC PEPTIDE, CHAINS CROSSLINKED COMPND 15 AT C-TERMINUS, CONTAINS J1-EPITOPE OF COLLAGEN TYPE II FROM MOUSE COMPND 16 FLANKED BY GPO REPEATS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 STRAIN: DBA/1; SOURCE 6 CELL_LINE: MURINE HYBRIDOMA (NS0); SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 9 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 10 ORGANISM_TAXID: 10090; SOURCE 11 STRAIN: DBA/1; SOURCE 12 CELL_LINE: MURINE HYBRIDOMA (NS0); SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 16 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 17 ORGANISM_TAXID: 10090 KEYWDS IMMUNE SYSTEM, ANTIBODY, RHEUMATOID ARTHRITIS, COLLAGEN TYPE II EXPDTA X-RAY DIFFRACTION AUTHOR B.RAPOSO,D.DOBRITZSCH,C.GE,D.EKMAN,I.LINDH,M.FOERSTER,H.UYSAL, AUTHOR 2 G.SCHNEIDER,R.HOLMDAHL REVDAT 4 20-DEC-23 4BKL 1 LINK REVDAT 3 26-MAR-14 4BKL 1 JRNL REVDAT 2 05-MAR-14 4BKL 1 JRNL REVDAT 1 05-FEB-14 4BKL 0 JRNL AUTH B.RAPOSO,D.DOBRITZSCH,C.GE,D.EKMAN,B.XU,I.LINDH,M.FORSTER, JRNL AUTH 2 H.UYSAL,K.S.NANDAKUMAR,G.SCHNEIDER,R.HOLMDAHL JRNL TITL EPITOPE-SPECIFIC ANTIBODY RESPONSE IS CONTROLLED BY JRNL TITL 2 IMMUNOGLOBULIN VH POLYMORPHISMS. JRNL REF J.EXP.MED. V. 211 405 2014 JRNL REFN ISSN 0022-1007 JRNL PMID 24534192 JRNL DOI 10.1084/JEM.20130968 REMARK 2 REMARK 2 RESOLUTION. 3.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 15468 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 823 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1097 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.3780 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.3820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3770 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 117.4 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.42000 REMARK 3 B22 (A**2) : 2.42000 REMARK 3 B33 (A**2) : -7.86000 REMARK 3 B12 (A**2) : 2.42000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 2.289 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.429 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.348 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.877 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3879 ; 0.009 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3497 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5294 ; 1.556 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8147 ; 1.745 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 503 ; 6.807 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;34.777 ;24.348 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 576 ;18.317 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;24.207 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 576 ; 0.160 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4400 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 812 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2027 ; 7.076 ;11.689 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2026 ; 7.064 ;11.688 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2525 ;10.886 ;17.503 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2526 ;10.885 ;17.506 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1852 ; 6.795 ;12.102 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1853 ; 6.793 ;12.104 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2770 ;10.820 ;17.978 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 14850 ;16.784 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 14848 ;16.783 ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 3 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 E 11 33 F 11 33 590 0.22 0.05 REMARK 3 2 E 11 33 G 11 33 605 0.23 0.05 REMARK 3 3 F 10 33 G 10 33 613 0.20 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. ONLY ONE OF THE TWO ALTERNATIVE CONFORMATION OF LOOP REMARK 3 A158-164 WAS MODELED SEVERAL RESIDUES AT THE C-TERMINUS OF FAB REMARK 3 HEAVY AND LIGHT CHAIN AND AT N- AND C-TERMINI OF THE PEPTIDE REMARK 3 CHAINS ARE NOT MODELED DUE TO LACK OF ELECTRON DENSITY REMARK 4 REMARK 4 4BKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-APR-13. REMARK 100 THE DEPOSITION ID IS D_1290056646. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.975 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16327 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.250 REMARK 200 RESOLUTION RANGE LOW (A) : 82.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.64000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2Y5T REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7 M AMMONIUM SULPHATE, 0.1 M HEPES REMARK 280 PH 7.0, 10 % DIOXANE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.47333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 126.94667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 126.94667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.47333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E, F, G REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 217 REMARK 465 PRO A 218 REMARK 465 ILE A 219 REMARK 465 SER A 220 REMARK 465 THR A 221 REMARK 465 ILE A 222 REMARK 465 ASN A 223 REMARK 465 PRO A 224 REMARK 465 CYS A 225 REMARK 465 PRO A 226 REMARK 465 PRO A 227 REMARK 465 CYS A 228 REMARK 465 LYS A 229 REMARK 465 GLU A 230 REMARK 465 CYS A 231 REMARK 465 GLU B 217 REMARK 465 CYS B 218 REMARK 465 GLY E 1 REMARK 465 PRO E 2 REMARK 465 HYP E 3 REMARK 465 GLY E 4 REMARK 465 PRO E 5 REMARK 465 HYP E 6 REMARK 465 GLY E 7 REMARK 465 PRO E 8 REMARK 465 HYP E 9 REMARK 465 GLY E 10 REMARK 465 HYP E 36 REMARK 465 GLY E 37 REMARK 465 GLY F 1 REMARK 465 PRO F 2 REMARK 465 HYP F 3 REMARK 465 GLY F 4 REMARK 465 PRO F 5 REMARK 465 HYP F 6 REMARK 465 GLY F 7 REMARK 465 PRO F 8 REMARK 465 PRO F 35 REMARK 465 HYP F 36 REMARK 465 GLY F 37 REMARK 465 GLY G 1 REMARK 465 PRO G 2 REMARK 465 HYP G 3 REMARK 465 GLY G 4 REMARK 465 PRO G 5 REMARK 465 HYP G 6 REMARK 465 GLY G 7 REMARK 465 PRO G 8 REMARK 465 HYP G 9 REMARK 465 PRO G 35 REMARK 465 HYP G 36 REMARK 465 GLY G 37 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL A 2 129.15 -38.30 REMARK 500 CYS A 22 76.08 -158.40 REMARK 500 SER A 88 -54.56 65.54 REMARK 500 ALA A 92 -168.26 170.99 REMARK 500 PHE B 32 -115.86 51.33 REMARK 500 PRO B 44 134.86 -36.86 REMARK 500 ALA B 55 -60.53 72.74 REMARK 500 GLN B 170 157.26 -47.89 REMARK 500 ASN B 194 -58.72 -121.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE ANTIBODY UNDERWENT SOMATIC MUTATION SEQUENCE IS REMARK 999 LARGELY IDENTICAL WITH THAT OF IGHV1-4 REMARK 999 THE ANTIBODY UNDERWENT SOMATIC MUTATION SEQUENCE IS REMARK 999 LARGELY IDENTICAL WITH THAT OF IGKV3-1 REMARK 999 ONE OF THE THREE PEPTIDE CHAINS HAS ADDITIONAL 4 RESIDUES REMARK 999 (KKYG) AT THE C-TERMINUS, WHICH CROSSLINKS ALL THREE CHAINS REMARK 999 WITH EACH OTHER WE HAVE NO WAY OF KNOWING WHICH OF THE 3 REMARK 999 CHAINS E, F OR G IT IS, DUE TO LACK OF ELECTRON DENSITY REMARK 999 FOR THE CROSSLINKED END DBREF 4BKL A 1 231 PDB 4BKL 4BKL 1 231 DBREF 4BKL B 1 218 PDB 4BKL 4BKL 1 218 DBREF 4BKL E 1 37 PDB 4BKL 4BKL 1 37 DBREF 4BKL F 1 37 PDB 4BKL 4BKL 1 37 DBREF 4BKL G 1 37 PDB 4BKL 4BKL 1 37 SEQRES 1 A 231 GLN VAL GLN LEU GLN GLN SER GLY ALA GLU LEU ALA LYS SEQRES 2 A 231 PRO GLY THR SER VAL LYS MET SER CYS LYS ALA SER GLY SEQRES 3 A 231 TYR THR PHE ILE SER TYR TRP MET ASN TRP VAL LYS GLN SEQRES 4 A 231 ARG PRO GLY GLN GLY LEU GLU TRP ILE GLY ALA ILE ASN SEQRES 5 A 231 PRO SER ASP GLY TYR THR GLU TYR ASN GLN LYS PHE LYS SEQRES 6 A 231 ASP LYS ALA ILE MET THR ALA ASP ARG SER SER SER THR SEQRES 7 A 231 ALA TYR MET GLN LEU SER SER LEU THR SER GLU ASP SER SEQRES 8 A 231 ALA LEU TYR TYR CYS ALA ARG TYR GLY GLY TYR PHE ASP SEQRES 9 A 231 TYR TRP GLY GLN GLY THR THR LEU THR VAL SER SER ALA SEQRES 10 A 231 LYS THR THR PRO PRO SER VAL TYR PRO LEU ALA PRO GLY SEQRES 11 A 231 CYS GLY ASP THR THR GLY SER SER VAL THR LEU GLY CYS SEQRES 12 A 231 LEU VAL LYS GLY TYR PHE PRO GLU SER VAL THR VAL THR SEQRES 13 A 231 TRP SER SER GLY SER LEU SER SER SER VAL HIS THR PHE SEQRES 14 A 231 PRO ALA LEU LEU GLN SER GLY LEU TYR THR MET SER SER SEQRES 15 A 231 SER VAL THR VAL PRO SER SER THR TRP PRO SER GLN THR SEQRES 16 A 231 VAL THR CYS SER VAL ALA HIS PRO ALA SER SER THR THR SEQRES 17 A 231 VAL ASP LYS LYS LEU GLU PRO SER GLY PRO ILE SER THR SEQRES 18 A 231 ILE ASN PRO CYS PRO PRO CYS LYS GLU CYS SEQRES 1 B 218 ASP ILE VAL LEU THR GLN SER PRO ALA SER LEU ALA VAL SEQRES 2 B 218 SER LEU GLY GLN ARG ALA THR ILE SER CYS ARG ALA SER SEQRES 3 B 218 GLU SER VAL GLU TYR PHE GLY THR SER LEU MET GLN TRP SEQRES 4 B 218 TYR GLN GLN LYS PRO GLY GLN PRO PRO LYS LEU LEU ILE SEQRES 5 B 218 TYR ALA ALA SER ASN VAL GLU SER GLY VAL PRO ALA ARG SEQRES 6 B 218 PHE SER GLY SER GLY SER GLY THR ASP PHE SER LEU ASN SEQRES 7 B 218 ILE HIS PRO VAL GLU GLU ASP ASP ILE ALA MET TYR PHE SEQRES 8 B 218 CYS GLN GLN SER ARG GLU VAL PRO TYR THR PHE GLY GLY SEQRES 9 B 218 GLY SER LYS LEU GLU ILE LYS ARG ALA ASP ALA ALA PRO SEQRES 10 B 218 THR VAL SER ILE PHE PRO PRO SER SER GLU GLN LEU THR SEQRES 11 B 218 SER GLY GLY ALA SER VAL VAL CYS PHE LEU ASN ASN PHE SEQRES 12 B 218 TYR PRO LYS ASP ILE ASN VAL LYS TRP LYS ILE ASP GLY SEQRES 13 B 218 SER GLU ARG GLN ASN GLY VAL LEU ASN SER TRP THR ASP SEQRES 14 B 218 GLN ASP SER LYS ASP SER THR TYR SER MET SER SER THR SEQRES 15 B 218 LEU THR LEU THR LYS ASP GLU TYR GLU ARG HIS ASN SER SEQRES 16 B 218 TYR THR CYS GLU ALA THR HIS LYS THR SER THR SER PRO SEQRES 17 B 218 ILE VAL LYS SER PHE ASN ARG ASN GLU CYS SEQRES 1 E 37 GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY SEQRES 2 E 37 PRO HYP GLY MET HYP GLY GLU ARG GLY ALA ALA GLY ILE SEQRES 3 E 37 ALA GLY PRO LYS GLY PRO HYP GLY PRO HYP GLY SEQRES 1 F 37 GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY SEQRES 2 F 37 PRO HYP GLY MET HYP GLY GLU ARG GLY ALA ALA GLY ILE SEQRES 3 F 37 ALA GLY PRO LYS GLY PRO HYP GLY PRO HYP GLY SEQRES 1 G 37 GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY SEQRES 2 G 37 PRO HYP GLY MET HYP GLY GLU ARG GLY ALA ALA GLY ILE SEQRES 3 G 37 ALA GLY PRO LYS GLY PRO HYP GLY PRO HYP GLY MODRES 4BKL HYP E 12 PRO 4-HYDROXYPROLINE MODRES 4BKL HYP E 15 PRO 4-HYDROXYPROLINE MODRES 4BKL HYP E 18 PRO 4-HYDROXYPROLINE MODRES 4BKL HYP E 33 PRO 4-HYDROXYPROLINE MODRES 4BKL HYP F 9 PRO 4-HYDROXYPROLINE MODRES 4BKL HYP F 12 PRO 4-HYDROXYPROLINE MODRES 4BKL HYP F 15 PRO 4-HYDROXYPROLINE MODRES 4BKL HYP F 18 PRO 4-HYDROXYPROLINE MODRES 4BKL HYP F 33 PRO 4-HYDROXYPROLINE MODRES 4BKL HYP G 12 PRO 4-HYDROXYPROLINE MODRES 4BKL HYP G 15 PRO 4-HYDROXYPROLINE MODRES 4BKL HYP G 18 PRO 4-HYDROXYPROLINE MODRES 4BKL HYP G 33 PRO 4-HYDROXYPROLINE HET HYP E 12 8 HET HYP E 15 8 HET HYP E 18 8 HET HYP E 33 8 HET HYP F 9 8 HET HYP F 12 8 HET HYP F 15 8 HET HYP F 18 8 HET HYP F 33 8 HET HYP G 12 8 HET HYP G 15 8 HET HYP G 18 8 HET HYP G 33 8 HETNAM HYP 4-HYDROXYPROLINE HETSYN HYP HYDROXYPROLINE FORMUL 3 HYP 13(C5 H9 N O3) HELIX 1 1 GLN A 62 LYS A 65 5 4 HELIX 2 2 PRO A 203 SER A 206 5 4 HELIX 3 3 GLU B 83 ILE B 87 5 5 HELIX 4 4 SER B 125 GLY B 132 1 8 HELIX 5 5 LYS B 187 HIS B 193 1 7 SHEET 1 AA 4 GLN A 3 GLN A 6 0 SHEET 2 AA 4 VAL A 18 SER A 25 -1 O LYS A 23 N GLN A 5 SHEET 3 AA 4 THR A 78 LEU A 83 -1 O ALA A 79 N CYS A 22 SHEET 4 AA 4 ALA A 68 ASP A 73 -1 O ILE A 69 N GLN A 82 SHEET 1 AB 4 GLU A 10 ALA A 12 0 SHEET 2 AB 4 THR A 110 VAL A 114 1 O THR A 111 N GLU A 10 SHEET 3 AB 4 ALA A 92 TYR A 99 -1 O ALA A 92 N LEU A 112 SHEET 4 AB 4 TYR A 105 TRP A 106 -1 O TYR A 105 N ARG A 98 SHEET 1 AC 6 GLU A 10 ALA A 12 0 SHEET 2 AC 6 THR A 110 VAL A 114 1 O THR A 111 N GLU A 10 SHEET 3 AC 6 ALA A 92 TYR A 99 -1 O ALA A 92 N LEU A 112 SHEET 4 AC 6 TRP A 33 GLN A 39 -1 O TRP A 33 N TYR A 99 SHEET 5 AC 6 LEU A 45 ILE A 51 -1 O GLU A 46 N LYS A 38 SHEET 6 AC 6 THR A 58 TYR A 60 -1 O GLU A 59 N ALA A 50 SHEET 1 AD 2 TYR A 105 TRP A 106 0 SHEET 2 AD 2 ALA A 92 TYR A 99 -1 O ARG A 98 N TYR A 105 SHEET 1 AE 4 SER A 123 LEU A 127 0 SHEET 2 AE 4 SER A 138 TYR A 148 -1 O GLY A 142 N LEU A 127 SHEET 3 AE 4 LEU A 177 PRO A 187 -1 O TYR A 178 N GLY A 147 SHEET 4 AE 4 VAL A 166 GLN A 174 -1 O HIS A 167 N SER A 183 SHEET 1 AF 3 THR A 154 TRP A 157 0 SHEET 2 AF 3 THR A 197 HIS A 202 -1 O SER A 199 N THR A 156 SHEET 3 AF 3 THR A 207 LYS A 212 -1 O THR A 207 N HIS A 202 SHEET 1 BA 4 LEU B 4 SER B 7 0 SHEET 2 BA 4 ALA B 19 ALA B 25 -1 O SER B 22 N SER B 7 SHEET 3 BA 4 ASP B 74 ILE B 79 -1 O PHE B 75 N CYS B 23 SHEET 4 BA 4 PHE B 66 SER B 71 -1 O SER B 67 N ASN B 78 SHEET 1 BB 4 SER B 10 SER B 14 0 SHEET 2 BB 4 LYS B 107 LYS B 111 1 O LYS B 107 N LEU B 11 SHEET 3 BB 4 ALA B 88 GLN B 94 -1 O ALA B 88 N LEU B 108 SHEET 4 BB 4 THR B 101 PHE B 102 -1 O THR B 101 N GLN B 94 SHEET 1 BC 6 SER B 10 SER B 14 0 SHEET 2 BC 6 LYS B 107 LYS B 111 1 O LYS B 107 N LEU B 11 SHEET 3 BC 6 ALA B 88 GLN B 94 -1 O ALA B 88 N LEU B 108 SHEET 4 BC 6 MET B 37 GLN B 42 -1 O GLN B 38 N GLN B 93 SHEET 5 BC 6 LYS B 49 TYR B 53 -1 O LYS B 49 N GLN B 41 SHEET 6 BC 6 ASN B 57 VAL B 58 -1 O ASN B 57 N TYR B 53 SHEET 1 BD 2 THR B 101 PHE B 102 0 SHEET 2 BD 2 ALA B 88 GLN B 94 -1 O GLN B 94 N THR B 101 SHEET 1 BE 2 GLU B 30 TYR B 31 0 SHEET 2 BE 2 THR B 34 SER B 35 -1 O THR B 34 N TYR B 31 SHEET 1 BF 4 THR B 118 PHE B 122 0 SHEET 2 BF 4 GLY B 133 PHE B 143 -1 O VAL B 137 N PHE B 122 SHEET 3 BF 4 TYR B 177 THR B 186 -1 O TYR B 177 N PHE B 143 SHEET 4 BF 4 VAL B 163 TRP B 167 -1 O LEU B 164 N THR B 182 SHEET 1 BG 4 SER B 157 GLU B 158 0 SHEET 2 BG 4 ILE B 148 ILE B 154 -1 O ILE B 154 N SER B 157 SHEET 3 BG 4 SER B 195 HIS B 202 -1 O THR B 197 N LYS B 153 SHEET 4 BG 4 SER B 205 ASN B 214 -1 O SER B 205 N HIS B 202 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.06 SSBOND 2 CYS A 143 CYS A 198 1555 1555 2.05 SSBOND 3 CYS B 23 CYS B 92 1555 1555 2.09 SSBOND 4 CYS B 138 CYS B 198 1555 1555 2.04 LINK C PRO E 11 N HYP E 12 1555 1555 1.35 LINK C HYP E 12 N GLY E 13 1555 1555 1.33 LINK C PRO E 14 N HYP E 15 1555 1555 1.34 LINK C HYP E 15 N GLY E 16 1555 1555 1.33 LINK C MET E 17 N HYP E 18 1555 1555 1.34 LINK C HYP E 18 N GLY E 19 1555 1555 1.33 LINK C PRO E 32 N HYP E 33 1555 1555 1.34 LINK C HYP E 33 N GLY E 34 1555 1555 1.34 LINK C HYP F 9 N GLY F 10 1555 1555 1.34 LINK C PRO F 11 N HYP F 12 1555 1555 1.35 LINK C HYP F 12 N GLY F 13 1555 1555 1.33 LINK C PRO F 14 N HYP F 15 1555 1555 1.34 LINK C HYP F 15 N GLY F 16 1555 1555 1.33 LINK C MET F 17 N HYP F 18 1555 1555 1.35 LINK C HYP F 18 N GLY F 19 1555 1555 1.33 LINK C PRO F 32 N HYP F 33 1555 1555 1.34 LINK C HYP F 33 N GLY F 34 1555 1555 1.33 LINK C PRO G 11 N HYP G 12 1555 1555 1.35 LINK C HYP G 12 N GLY G 13 1555 1555 1.33 LINK C PRO G 14 N HYP G 15 1555 1555 1.34 LINK C HYP G 15 N GLY G 16 1555 1555 1.33 LINK C MET G 17 N HYP G 18 1555 1555 1.34 LINK C HYP G 18 N GLY G 19 1555 1555 1.33 LINK C PRO G 32 N HYP G 33 1555 1555 1.34 LINK C HYP G 33 N GLY G 34 1555 1555 1.33 CISPEP 1 PHE A 149 PRO A 150 0 1.06 CISPEP 2 TRP A 191 PRO A 192 0 6.27 CISPEP 3 SER B 7 PRO B 8 0 2.84 CISPEP 4 HIS B 80 PRO B 81 0 1.31 CISPEP 5 VAL B 98 PRO B 99 0 -0.08 CISPEP 6 TYR B 144 PRO B 145 0 1.47 CRYST1 95.180 95.180 190.420 90.00 90.00 120.00 P 31 2 1 18 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.010506 0.006066 0.000000 0.00000 SCALE2 0.000000 0.012132 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005252 0.00000